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<title>WebLogo - Logo Form Help</title>
<meta name="author" content="Gavin E. Crooks" />
<meta name="ID" content="$ID:" />
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<h1>
  <a class="in" href="./"><img alt="WebLogo" width="146" height="65"  border="0" src="img/weblogologo.png" /></a>
  BETA
  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
  &middot; 
  <a href="">about</a>&nbsp;&middot;
  <a class="selected" href="logo.cgi">create</a>&nbsp;&middot; 
  <a href="examples.html">examples</a>&nbsp;&middot; 
</h1>

<h3>Logo Creation Form Help</h3>


<dl>

<dt><a name="msa">Multiple Sequence Alignment</a></dt>
<dd>
Enter your sequence information here. There are three formats to choose from; 
<a href="#fasta">FASTA</a>,  <a href="#clustalw">CLUSTALW</a>, and <a href="#flat">flat</a>.
In all cases, lines beginning with "#" are comment lines
and have no effect on the output logo. All sequences must be the same length.

<br /><br />

<dl>
  <dt><a name="fasta">FASTA format:</a></dt>
  <dd>
<pre><code>  >name1 (optional)
  acgtacgtacgtacgtacgattca
  >name2 (optional)
  tacgtacgatcgatcgtgactacg
  >name3 (optional)
  actgactagctactagctactacg
  ... 
  >nameN (optional)
  actgactagctagcatcgactgac
</code></pre>
  </dd>
  <dt><br /><a name="clustaw">CLUSTALW format:</a></dt>
  <dd>
<pre><code>  name1line1      atcgagttatcgcgaggagaggcgcgtacgatcgatcgatcgatgcatgcatcgatcgatgctataatacgatgctagca
  name2line1      tacgtacgatcgatcgtgactacgactgatcgatgcatcgatgctagctagctagctagctagctagcatgctagctagc
  ...
  nameNline1      actgactagctagcatcgactgacactgactgactgatcgatcgatcgatcgatcgatcgatcgatcgatcgtagtagtg
  name1line2      atgcatcgacacacatgtgtgatcattatagagcgctagcatgcatgctagatcgtacgtacgtacgtacgtacgattca
  name2line2      tacgtacgatcgatcgtgactacgatgcatgcatcgcggatatatagagagatctatcgcatcgatcgatcgatcgatcg
  ...             atcgagttatcgcgaggagaggcgcgtacgatcgatcgatcgatgcatgcatcgatcgatgctataatacgatgctagca
  nameNline2      actgactagctagcatcgactgacatcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatgctagctagc
  ...
  ...
  name1lineM      acgtacgtacgtacgtacg
  name2lineM      tacgtacgatcgatcgtga
  ...
  nameNlineM      actgactagctagcatcga
</code></pre>
  </dd>
  <dt><br /><a name="clustaw">Flat format (each sequence must be of same length):</a></dt>
  <dd>
<pre><code>  sequence1
  sequence2
  sequence3
  ...
  sequenceN
</code></pre>
  </dd>
</dl>

</dd>



<!--
<dt><a name="upload">Upload Sequence Data</a></dt>
<br />
<dd>
Not supported yet
</dd>
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<dt><a name="seqtype">Sequence Type</a></dt>
<dd>
Sequence data can be of "amino acid" or "DNA/RNA". Choose 
"Automatic Detection" to have Weblogo choose for you, based on the entered
data (if 90% or more of the entered data are a, c, t or g residues, then
Weblogo chooses DNA/RNA.
</dd>


<dt><a name="ends">Label Sequence Ends</a></dt>
<dd> 
Choose this option to label the 5' &amp; 3' ends of nucleic acid or 
the N &amp; C termini of amino acid sequences.
</dd>


<dt><a name="firstnum">First Position Number</a></dt>
<dd>
The numerical label of the first residue in the multiple sequence alignment.
The label must be an integer.
Residue labels for the logo will be relative to this number. 
(See also: <a href = "#range">Logo Range</a>)
</dd>

<dt><a name="range">Logo Range</a></dt>
<dd>
By default, all sequence data is displayed in the Sequence Logo. With 
this option, you can instead show a subrange of the entire sequence. Start
and end positions are included,
and the numbering of positions is relative to the sequence number of the 
first position. (See also: <a href="#firstnum">First Position Number</a> )
Thus, if the first position number is "2", start is "5" and end is "10", then
the 4th through 9th (inclusive) sequence positions will be displayed, and 
they will be numbered "5", "6", "7", "8", "9" and "10".
</dd>

<dt><a name="uniform">Frequency Plot</a></dt>
<dd>
Show residue frequencies, rather than information content.
</dd>



<dt><a name="ssc">Small Sample Correction</a></dt>
<dd>
When there are only a few sample sequences a straightforward calculation 
will tend to overestimate the entropy. To compensate, this option will
subtract an approximation of this bias from the total entropy.
This small sample correction depends only
on the number of symbol types (4 for RNA/DNA, 20 for protein) and
the total amount of data in each column, which may differ from
one column to another, since some columns will contain more gaps,
and less data.
</dd>

<dt><a name="multiline">Multiline Logos</a></dt>
<dd>
A multiline Logo will split the sequence across several lines, instead of 
cramming
all of the sequence within the single line width specified above. 
The Logo height specified at the top of the form becomes
the height of each Logo line.
The number of logo characters per line can be specified.
</dd>

<dt><a name="errbar">Error Bars</a></dt>
<dd>
The total height of the error bar is twice the small sample correction.
</dd>

<dt><a name="format">Image Format</a></dt>
<dd>
The logo can be output in several formats. The following are currently
supported:
<ul>
  <li>EPS : Adobe Encapsulated PostScript</li>
  <li>GIF : CompuServe Graphics Interchange Format</li>
  <li>PNG : Portable Network Graphics</li>
  <li>PDF : Adobe Portable Document Format</li>
</ul>

Generally speaking, vector formats (EPS and PDF) are better for printing,
while bitmaps (GIF and PNG) are more suitable for displaying on the screen, or
embedding into a web page.
</dd>

<dt><a name="size">Logo Size</a></dt>
<dd>
Physical dimensions of output logo in centimeters, inches, pixels, or points.
</dd>

<dt><a name="res">Bitmap Resolution</a></dt>
<dd>
Typical values are 72 pixels/inch for screen display under Mac OS,
96 pixels/inch for screen display under Windows and 300 or 600
pixels/inch for output to a laser printer.
</dd>

<dt><a name="antialias">Antialias Bitmaps</a></dt>
<dd>
  Antialiasing smoothes the rough edges on a bitmap. You may wish to disable
  this feature if, for example, you intend to further edit the bitmap.
</dd>

<dt><a name="title"></a>Title</dt>
<dd>
Give your logo a title.
</dd>

<dt><a name="barbits">Y-axis Height</a></dt>
<dd>
  Specify the number of bits on the y axis.
  By default, the height of the y-axis is
  the maximum entropy for the given sequence type.
  (log<sub>2</sub>&nbsp;4&nbsp;=&nbsp;2&nbsp;bits for DNA/RNA, 
  log<sub>2</sub>&nbsp;20&nbsp;=&nbsp;4.3&nbsp;bits for protein.)
</dd>

<dt><a name="yaxis">Show Y-Axis</a></dt>
<dd>
  The vertical axis indicates the information content of a 
  sequence position, in bits. Use this option to toggle the y-axis 
  and its bit labels.
</dd>

<dt><a name="yaxis_label">Y-Axis Label</a></dt>
<dd>
  Give your y-axis a name. The default label for the y-axis is "bits".
</dd>

<dt><a name="xaxis">Show X-Axis</a></dt>
<dd>
  The horizontal axis indicates the residue number. Use this option to
  toggle the x-axis and its labels.
</dd>

<dt><a name="xaxis_label">X-Axis Label</a></dt>
<dd>
  Customize your x-axis's label. The default is no label.
</dd>

<dt><a name="boxed">Boxed Symbols</a></dt>
<dd>
  It is sometimes useful to outline logo residues with boxes.  Use the
  the shrink factor to decrease the residue size by the factor specified. 
  The default shrink factor is 0.5, 
  meaning halve the residue size.
</dd>

<dt><a name="outline">Outline</a></dt>
<dd>
  By default, the logo residues are filled. Use this option to get outlined 
 (non-filled) residues.
</dd>

<dt><a name="colors">Color Scheme</a></dt>
<dd>
The default colors for nucleic acids are 
G, orange; T &amp; U, red; C, blue; and A, green.
Amino acids are colored according to their chemical
properties: polar amino acids (G,S,T,Y,C,Q,N) are green, 
basic (K,R,H) blue, acidic (D,E) red and
hydrophobic (A,V,L,I,P,W,F,M) amino acids are black.
Alternatively, the Black &amp; White option will color 
all symbols black, or the default color scheme can be
overridden with the custom colors specified below. 


<dl>
  <dt><a name="color_sym">Symbols</a></dt>
  <dd>
    Specify the residue letters here. The symbols are case insensitive. 
    No repeated residues are allowed.
  </dd>

  <dt><a name="color_color">Colors</a></dt>
  <dd>
    Choose the color to give the residues specified in <a href = "#color_sym">
    "Symbols" </a>. Use the drop-down list to:
    <br />&nbsp;&nbsp;&nbsp; * choose a pre-defined color (Black, Red, Green,
    Blue, Yellow, Purple, or Orange) or
    <br />&nbsp;&nbsp;&nbsp; * choose "RGB=>" and specify an appropriate RGB
    color in the <a href = "#color_RGB"> "RGB" </a> field.
  </dd>

  <dt><a name="color_RGB">RGB</a></dt>
  <dd>
    If you chose "RGB=>" in the <a href = "#color_color"> "Colors" </a> field,
    specify standard hexadecimal colors here
    (e.&nbsp;g. FF0000 for pure red, 006666 for Slashdot green).
  </dd>
</dl>
</dd>


<!--
<dt><a name="">Symbols per Logo line</a></dt>
<dd>
A multiline Logo will split the sequence across several lines, instead of 
cramming
all of the sequence within the single line width specified above. 
The Logo height specified at the top of the form becomes
the height of each Logo line.
</dd>
<dt>
-->

</dl>
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<div align="center">
<address>
<a href="mailto:logo@compbio.berkeley.edu">logo@</a><a 
href="http://compbio.berkeley.edu/">The Holy Science Palace</a></address>
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